What matters is whether you had a valid travel document at the time of the check and were able to produce it within the time required by the check. For example, if there were technical problems (mobile phone out of charge, signal failure, etc.), it depends on the rules of the particular carrier and the reasonableness of its procedure. The Road Transport Act and the timetables usually stipulate that the passenger must carry the travel document and produce it immediately on request.
If you had a valid ticket and presented it at least subsequently as part of a claim, we recommend that you object to the fine. If the carrier does not forgive the fine, you can appeal to the Czech Trade Inspectorate or, if you consider the fine unjustified, to the court.